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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ), 'gf_id' => 'HOM05D001620', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001620' ), 'data_identifier' => 'HOM05D001620', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001620', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p05050' => 'bna', 'A06p20680' => 'bna', 'Aa31LG2G50' => 'aar', 'Aa31LG4G15800' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3808' => 'aag', 'Actinidia17986' => 'ach', 'Actinidia20585' => 'ach', 'Actinidia22372' => 'ach', 'Actinidia24457' => 'ach', 'Ah.01g004170' => 'amhyb', 'Ah.06g194630' => 'amhyb', 'Ah.07g202490' => 'amhyb', 'AL2G13550' => 'aly', 'AL5G25890' => 'aly', 'AL6G19720' => 'aly', 'Aqoxy1G00797' => 'aox', 'Aqoxy1G01291' => 'aox', 'Aqoxy5G00121' => 'aox', 'Aqoxy6G02985' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C9A28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6U9V59' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DZXH0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E1XKB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0W8DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UZY3CQ' => 'arhy', 'AT1G62350' => 'ath', 'AT3G46870' => 'ath', 'AT5G09315' => 'ath', 'ATR0605G005' => 'atr', 'ATR0605G201' => 'atr', 'ATR0705G003' => 'atr', 'ATR0743G151' => 'atr', 'ATR0743G190' => 'atr', 'Atru.chr3.2949' => 'acertr', 'Atru.chr3.2960' => 'acertr', 'Atru.chr3.4027' => 'acertr', 'Atru.chr4.1349' => 'acertr', 'Atru.chr5.3578' => 'acertr', 'AUR62000196' => 'cqu', 'AUR62000199' => 'cqu', 'AUR62002271' => 'cqu', 'AUR62002366' => 'cqu', 'AUR62006547' => 'cqu', 'AUR62023819' => 'cqu', 'AUR62037326' => 'cqu', 'AUR62037709' => 'cqu', 'AUR62038966' => 'cqu', 'BcaB01g00964' => 'bca', 'BcaB02g06699' => 'bca', 'BcaB08g37218' => 'bca', 'BcaC01g01878' => 'bca', 'BcaC05g24711' => 'bca', 'BolC3t19384H' => 'bol', 'BolC5t29360H' => 'bol', 'BolC9t54888H' => 'bol', 'BraA06t23711Z' => 'bra', 'BraA06t25147Z' => 'bra', 'C03p71020' => 'bna', 'C05p05990' => 'bna', 'C09p19830' => 'bna', 'CAN.G1155.34' => 'can', 'CAN.G1186.27' => 'can', 'CAN.G234.1' => 'can', 'CAN.G674.10' => 'can', 'CANSAT25G0192' => 'cansat', 'CANSAT25G1898' => 'cansat', 'CANSAT54G0541' => 'cansat', 'CANSAT54G0752' => 'cansat', 'CARHR049570' => 'chi', 'CARHR155520' => 'chi', 'CARHR204080' => 'chi', 'Carub.0002s0263' => 'cru', 'Carub.0005s1308' => 'cru', 'Ca_01237_v3' => 'car', 'Ca_17989_v3' => 'car', 'Ca_20610_v3' => 'car', 'Ca_29564_v3' => 'car', 'Cc00_g03540' => 'ccan', 'Cc00_g25090' => 'ccan', 'Cc00_g29970' => 'ccan', 'Cc02_g31900' => 'ccan', 'Cc03_g11940' => 'ccan', 'Cc03_g12150' => 'ccan', 'Cc09_g06110' => 'ccan', 'CDE02G0743' => 'cde', 'CDE04G3108' => 'cde', 'CDE04G3660' => 'cde', 'CDE08G0938' => 'cde', 'Cfa005393' => 'cfa', 'Cfa009879' => 'cfa', 'Cfa011584' => 'cfa', 'Cfa015222' => 'cfa', 'Ciclev10016520m.g' => 'ccl', 'Ciclev10021852m.g' => 'ccl', 'Ciclev10029031m.g' => 'ccl', 'Ciclev10029104m.g' => 'ccl', 'CiPaw.01G173100' => 'cil', 'CiPaw.05G094900' => 'cil', 'CiPaw.13G087400' => 'cil', 'CiPaw.13G149900' => 'cil', 'ClCG02G003250' => 'cla', 'ClCG03G001190' => 'cla', 'ClCG03G012540' => 'cla', 'ClCG07G015080' => 'cla', 'COL.COLO4_03849' => 'col', 'COL.COLO4_18601' => 'col', 'COL.COLO4_28387' => 'col', 'COL.COLO4_29868' => 'col', 'Cpa.g.sc69.1' => 'cpa', 'Cpa.g.sc81.55' => 'cpa', 'Cpa.g.sc9.334' => 'cpa', 'Cpa.g.sc96.35' => 'cpa', 'CsaV3_1G034610' => 'csa', 'CsaV3_1G035710' => 'csa', 'CsaV3_1G043490' => 'csa', 'CsaV3_4G002630' => 'csa', 'CsaV3_7G002140' => 'csa', 'CSS0013600' => 'camsi', 'CSS0013648' => 'camsi', 'CSS0032693' => 'camsi', 'DCAR_018331' => 'dca', 'DCAR_020026' => 'dca', 'DCAR_029911' => 'dca', 'Dinv14184' => 'din', 'Dinv15033' => 'din', 'Dinv25389' => 'din', 'Dinv31490' => 'din', 'Dinv44168' => 'din', 'Duzib150G0940' => 'dzi', 'Duzib168G0729' => 'dzi', 'Duzib212G0571' => 'dzi', 'ECA233G0963' => 'eca', 'ECA236G2477' => 'eca', 'ECA238G3542' => 'eca', 'ECA240G1247' => 'eca', 'ECA240G4634' => 'eca', 'EL10Ac3g06031' => 'bvu', 'EL10Ac4g10112' => 'bvu', 'EL10Ac9g20788' => 'bvu', 'Eucgr.A00027' => 'egr', 'Eucgr.A00032' => 'egr', 'Eucgr.A00034' => 'egr', 'Eucgr.B02297' => 'egr', 'Eucgr.B03737' => 'egr', 'Eucgr.H05004' => 'egr', 'FAN11G0333' => 'fan', 'FAN11G2079' => 'fan', 'FAN15G2752' => 'fan', 'FAN16G1201' => 'fan', 'FAN16G2458' => 'fan', 'FAN21G0292' => 'fan', 'FAN21G2221' => 'fan', 'FAN24G0497' => 'fan', 'FAN25G1449' => 'fan', 'FAN25G3321' => 'fan', 'FAN27G0152' => 'fan', 'FvH4_2g17040' => 'fve', 'FvH4_3g28730' => 'fve', 'FvH4_3g37180' => 'fve', 'Glyma.07G164700' => 'gma', 'Glyma.11G135100' => 'gma', 'Glyma.12G058700' => 'gma', 'Glyma.13G341300' => 'gma', 'Glyma.15G027600' => 'gma', 'Glyma.15G269900' => 'gma', 'Glyma.18G047500' => 'gma', 'Gohir.A02G092600' => 'ghi', 'Gohir.A03G170100' => 'ghi', 'Gohir.A05G092100' => 'ghi', 'Gohir.A13G218600' => 'ghi', 'Gohir.D02G110700' => 'ghi', 'Gohir.D02G193200' => 'ghi', 'Gohir.D05G092900' => 'ghi', 'Gohir.D13G222300' => 'ghi', 'Gorai.005G125600' => 'gra', 'Gorai.005G216000' => 'gra', 'Gorai.009G095500' => 'gra', 'Gorai.013G253400' => 'gra', 'GSVIVG01023856001' => 'vvi', 'GSVIVG01024591001' => 'vvi', 'GSVIVG01024855001' => 'vvi', 'GSVIVG01037289001' => 'vvi', 'GSVIVG01038096001' => 'vvi', 'HanXRQChr03g0093541' => 'han', 'HanXRQChr06g0167661' => 'han', 'HanXRQChr08g0227601' => 'han', 'HanXRQChr13g0419631' => 'han', 'Haze_01411' => 'cav', 'Haze_01412' => 'cav', 'Haze_01414' => 'cav', 'Haze_01957' => 'cav', 'Haze_12936' => 'cav', 'Haze_23244' => 'cav', 'Haze_24202' => 'cav', 'Hma1.2p1_0619F.1_g190430' => 'hma', 'Hma1.2p1_0837F.1_g226100' => 'hma', 'Hma1.2p1_2359F.1_g320596' => 'hma', 'HPP92_003237' => 'vpl', 'HPP92_008154' => 'vpl', 'HPP92_013691' => 'vpl', 'HPP92_013768' => 'vpl', 'HPP92_013840' => 'vpl', 'HPP92_013857' => 'vpl', 'Hund01063' => 'sun', 'Hund03188' => 'sun', 'Hund11612' => 'sun', 'Hund21976' => 'sun', 'Lalb_Chr10g0096181' => 'lal', 'Lalb_Chr19g0138011' => 'lal', 'Lalb_Chr23g0275861' => 'lal', 'Lj2A378T24' => 'lonja', 'Lj2g0012959' => 'lja', 'Lj3C1022T9' => 'lonja', 'Lj3g0024858' => 'lja', 'Lj4g0021462' => 'lja', 'Lj5P170T30' => 'lonja', 'Lsat_1_v5_gn_2_31920' => 'lsa', 'Lsat_1_v5_gn_3_109820' => 'lsa', 'Lsat_1_v5_gn_4_71240' => 'lsa', 'Lsat_1_v5_gn_6_13640' => 'lsa', 'Lsat_1_v5_gn_8_55121' => 'lsa', 'Manes.02G126700' => 'mes', 'Manes.11G012200' => 'mes', 'Manes.11G127400' => 'mes', 'Manes.15G113700' => 'mes', 'Mapoly0001s0141' => 'mpo', 'Mapoly0033s0149' => 'mpo', 'MBI01_g28400_MAGBIO' => 'mbi', 'MBI02_g35316_MAGBIO' => 'mbi', 'MBI07_g02902_MAGBIO' => 'mbi', 'MBI15_g18583_MAGBIO' => 'mbi', 'MBI17_g25734_MAGBIO' => 'mbi', 'MD03G1083200' => 'mdo', 'MD04G1047000' => 'mdo', 'MD10G1143100' => 'mdo', 'MD11G1091300' => 'mdo', 'MD11G1091600' => 'mdo', 'MD11G1091700' => 'mdo', 'MD11G1184300' => 'mdo', 'MD11G1184600' => 'mdo', 'Medtr1g031110' => 'mtr', 'Medtr2g099410' => 'mtr', 'Medtr3g079890' => 'mtr', 'Medtr3g079970' => 'mtr', 'Medtr4g064917' => 'mtr', 'MELO3C015110.2' => 'cme', 'MELO3C015694.2' => 'cme', 'MELO3C017777.2' => 'cme', 'MELO3C020598.2' => 'cme', 'Migut.B00943' => 'egut', 'Migut.M01344' => 'egut', 'Migut.N02375' => 'egut', 'Migut.N03083' => 'egut', 'MSTRG.11140' => 'ama', 'MSTRG.11478' => 'ama', 'MSTRG.16958' => 'ama', 'MSTRG.22018' => 'ama', 'Nitab4.5_0000446g0140' => 'nta', 'Nitab4.5_0000697g0200' => 'nta', 'Nitab4.5_0001481g0050' => 'nta', 'Nitab4.5_0001700g0020' => 'nta', 'Nitab4.5_0002421g0040' => 'nta', 'Nitab4.5_0005704g0010' => 'nta', 'Nitab4.5_0007459g0010' => 'nta', 'Nitab4.5_0008172g0010' => 'nta', 'Nn1g08939' => 'nnu', 'Nn3g20027' => 'nnu', 'Nn6g31636' => 'nnu', 'Nn7g37619' => 'nnu', 'Oeu013082.3' => 'oeu', 'Oeu015935.2' => 'oeu', 'Oeu020798.1' => 'oeu', 'Oeu048110.1' => 'oeu', 'Oeu064131.1' => 'oeu', 'Oeu064132.1' => 'oeu', 'Os03g0297700' => 'osa', 'Os04g0475500' => 'osa', 'Os07g0549200' => 'osa', 'Peaxi162Scf00047g00009' => 'pax', 'Peaxi162Scf00126g00612' => 'pax', 'Peaxi162Scf00126g00627' => 'pax', 'Peaxi162Scf00126g00814' => 'pax', 'Peaxi162Scf00374g00732' => 'pax', 'Peaxi162Scf00486g00097' => 'pax', 'PGR014G0005' => 'pgr', 'PGR083G0805' => 'pgr', 'PGR102G0575' => 'pgr', 'PGR102G2136' => 'pgr', 'PGSC0003DMG400016831' => 'stu', 'PGSC0003DMG400018809' => 'stu', 'PGSC0003DMG400020592' => 'stu', 'PGSC0003DMG400022873' => 'stu', 'PGSC0003DMG401018810' => 'stu', 'Phvul.003G032700' => 'pvu', 'Phvul.005G155600' => 'pvu', 'Phvul.011G060800' => 'pvu', 'Potri.001G275000' => 'ptr', 'Potri.007G134300' => 'ptr', 'Potri.009G038200' => 'ptr', 'Potri.009G169600' => 'ptr', 'Pp3c6_14920' => 'ppa', 'Prupe.1G201600' => 'ppe', 'Prupe.4G265100' => 'ppe', 'Prupe.6G067500' => 'ppe', 'Prupe.8G182100' => 'ppe', 'Psat5g291680' => 'psa', 'Psat6g043200' => 'psa', 'Psat7g211240' => 'psa', 'PSO339G4667' => 'pso', 'PSO349G0137' => 'pso', 'PSO541G2761' => 'pso', 'PSO675G0461' => 'pso', 'PSO675G1501' => 'pso', 'PSO765G0157' => 'pso', 'QL01p017010' => 'qlo', 'QL01p028186' => 'qlo', 'QL10p052582' => 'qlo', 'QL11p056803' => 'qlo', 'RcHm_v2.0_Chr5g0052331' => 'rch', 'RcHm_v2.0_Chr5g0066921' => 'rch', 'RcHm_v2.0_Chr6g0281221' => 'rch', 'Rhsim07G0068400' => 'rsi', 'Rhsim07G0221500' => 'rsi', 'Rhsim13G0208800' => 'rsi', 'Sabra07G0109000' => 'sbr', 'Sabra09G0027200' => 'sbr', 'Sabra09G0052400' => 'sbr', 'Sabra09G0131500' => 'sbr', 'Sabra16G0169300' => 'sbr', 'Sabra16G0169500' => 'sbr', 'SalBow1G8418' => 'sbo', 'SalBow6G2343' => 'sbo', 'SalBow8G2071' => 'sbo', 'Sc06g0004700' => 'sci', 'Sc07g0007120' => 'sci', 'Sc18g0005700' => 'sci', 'Sc19g0002780' => 'sci', 'Sed0006894' => 'sed', 'Sed0016023' => 'sed', 'Sed0025758' => 'sed', 'Sed0027002' => 'sed', 'SEGI_01800' => 'sgi', 'SEGI_06390' => 'sgi', 'SEGI_13321' => 'sgi', 'SEGI_20759' => 'sgi', 'SEGI_36684' => 'sgi', 'SEGI_37669' => 'sgi', 'SGA_v2.0_scaffold104G30256' => 'sas', 'SGA_v2.0_scaffold25G10993' => 'sas', 'SGA_v2.0_scaffold298G47714' => 'sas', 'SGA_v2.0_scaffold310G48202' => 'sas', 'SGA_v2.0_scaffold7G03803' => 'sas', 'SHI25415' => 'shi', 'SMO172G0041' => 'smo', 'SMO347G0066' => 'smo', 'SMO347G0172' => 'smo', 'SMO347G0380' => 'smo', 'SMO351G0245' => 'smo', 'Solyc08g061590.4' => 'sly', 'Solyc09g092360.3' => 'sly', 'Solyc10g074600.3' => 'sly', 'Solyc11g045220.2' => 'sly', 'Sopen08g017040' => 'spe', 'Sopen09g035260' => 'spe', 'Sopen10g027090' => 'spe', 'Sopen11g020680' => 'spe', 'Sp2g02250' => 'spa', 'Sp5g14880' => 'spa', 'Sp6g34000' => 'spa', 'TAR365G0548' => 'tar', 'TAR369G0223' => 'tar', 'TAR376G0870' => 'tar', 'TAR633G0723' => 'tar', 'THA.LOC104799129' => 'tha', 'THA.LOC104800065' => 'tha', 'THA.LOC104810746' => 'tha', 'Thecc.02G148000' => 'tca', 'Thecc.04G171200' => 'tca', 'Thecc.09G247800' => 'tca', 'Thecc.09G312600' => 'tca', 'Thhalv10010650m.g' => 'esa', 'Thhalv10023910m.g' => 'esa', 'TPR.G20396' => 'tpr', 'TPR.G22628' => 'tpr', 'TPR.G23569' => 'tpr', 'TPR.G36872' => 'tpr', 'TWI38G2083' => 'twi', 'TWI56G1405' => 'twi', 'TWI75G1254' => 'twi', 'TWI79G0573' => 'twi', 'unitig_744.g24613' => 'ugi', 'vmacro04039' => 'vma', 'vmacro13763' => 'vma', 'VMungo0171G0001' => 'vmu', 'VMungo0720G2846' => 'vmu', 'VMungo1127G0017' => 'vmu', 'Zm00001eb079800' => 'zma', 'Zm00001eb106590' => 'zma', 'Zm00001eb144720' => 'zma' ) $gf_id = 'HOM05D001620' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001620' ) $data_identifier = 'HOM05D001620' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 5, 'bol' => (int) 3, 'bra' => (int) 2, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 2, 'car' => (int) 4, 'ccan' => (int) 7, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 7, 'hma' => (int) 3, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb144720' $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